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annotate CADDSuite-1.5/galaxyconfigs/tools/ProteinProtonator.xml @ 7:bfab27640f5e draft

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CADDSuite version 1.5
author Marcel Schumann <schumann.marcel@gmail.com>
date Tue, 24 Jul 2012 11:13:59 -0400
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2 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
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3 <tool id="proteinprotonator" name="ProteinProtonator" version="1.5">
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4 <description>protonate protein structures</description>
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5 <command interpreter="bash"><![CDATA[../../ProteinProtonator
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6 #if str( $i ) != '' and str( $i ) != 'None' :
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7 -i "$i"
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8 #end if
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9 #if str( $o ) != '' and str( $o ) != 'None' :
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10 -o "$o"
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11 #end if
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12 #if str( $ph ) != '' and str( $ph ) != 'None' :
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13 -ph "$ph"
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14 #end if
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15 | tail -n 5
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16 ]]></command>
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17 <inputs>
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18 <param name="i" optional="false" label="input file" type="data" format="pdb"/>
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19 <param name="ph" optional="true" label="Optional: pH-value for pH-dep. protonation" type="text" area="true" size="1x5" value="7.0"/>
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20 </inputs>
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21 <outputs>
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22 <data name="o" format="pdb" format_source="i"/>
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23 </outputs>
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24 <help>ProteinProtonator allows you add hydrogens to a protein structure.
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26 Note that all hydrogen atoms already present in the input file will be ignored. If desired, you can specify a specific pH value, for which protonation is to be done; otherwise a neutral pH will be assumed.
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28 Output of this tool is one pdb-file containing the input protein structure with added hydrogens atoms.</help>
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29 </tool>